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(-) Description

Title :  CRYSTAL STRUCTURE OF ANTI-INFLUENZA VIRUS ANTIBODY 1F1
 
Authors :  D. C. Ekiert, I. A. Wilson
Date :  04 Sep 12  (Deposition) - 19 Dec 12  (Release) - 26 Dec 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.45
Chains :  Asym. Unit :  H,I,L,M
Biol. Unit 1:  H,L  (1x)
Biol. Unit 2:  I,M  (1x)
Keywords :  Immunoglobulin, Immune Recognition, Immune System (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  T. Tsibane, D. C. Ekiert, J. C. Krause, O. Martinez, J. E. Crowe, I. A. Wilson, C. F. Basler
Influenza Human Monoclonal Antibody 1F1 Interacts With Thre Major Antigenic Sites And Residues Mediating Human Receptor Specificity In H1N1 Viruses.
Plos Pathog. V. 8 03067 2012
PubMed-ID: 23236279  |  Reference-DOI: 10.1371/JOURNAL.PPAT.1003067

(-) Compounds

Molecule 1 - ANTIBODY 1F1, HEAVY CHAIN
    Chains: H, I
    Engineered: YES
    Expression System: HOMO SAPIENS
    Expression System Common: HUMAN
    Expression System Strain: 293 FREESTYLE
    Expression System Taxid: 9606
    Expression System Vector Type: PLASMID
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
 
Molecule 2 - ANTIBODY 1F1, LIGHT CHAIN
    Chains: L, M
    Engineered: YES
    Expression System: HOMO SAPIENS
    Expression System Common: HUMAN
    Expression System Strain: 293 FREESTYLE
    Expression System Taxid: 9606
    Expression System Vector Type: PLASMID
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : HILM
Biological Unit 1 (1x): H L 
Biological Unit 2 (1x):  I M

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 4)

Asymmetric Unit (1, 4)
No.NameCountTypeFull Name
1PCA4Mod. Amino AcidPYROGLUTAMIC ACID
Biological Unit 1 (1, 2)
No.NameCountTypeFull Name
1PCA2Mod. Amino AcidPYROGLUTAMIC ACID
Biological Unit 2 (1, 2)
No.NameCountTypeFull Name
1PCA2Mod. Amino AcidPYROGLUTAMIC ACID

(-) Sites  (0, 0)

(no "Site" information available for 4GXV)

(-) SS Bonds  (8, 8)

Asymmetric Unit
No.Residues
1H:22 -H:92
2H:140 -H:196
3I:22 -I:92
4I:140 -I:196
5L:23 -L:88
6L:134 -L:193
7M:23 -M:88
8M:134 -M:193

(-) Cis Peptide Bonds  (6, 6)

Asymmetric Unit
No.Residues
1Phe H:146 -Pro H:147
2Glu H:148 -Pro H:149
3Tyr L:140 -Pro L:141
4Phe I:146 -Pro I:147
5Glu I:148 -Pro I:149
6Tyr M:140 -Pro M:141

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4GXV)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4GXV)

(-) Exons   (0, 0)

(no "Exon" information available for 4GXV)

(-) Sequences/Alignments

Asymmetric Unit
   Reformat: Number of residues per line =  ('0' or empty: single-line sequence representation)
  Number of residues per labelling interval =   
  UniProt sequence: complete  aligned part    
   Show mapping: SCOP domains CATH domains Pfam domains Secondary structure (by author)
SAPs(SNPs) PROSITE motifs Exons
(details for a mapped element are shown in a popup box when the mouse pointer rests over it) 
Chain H from PDB  Type:PROTEIN  Length:228
                                                                                                                                                                                                                                                                     
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..eeeee..eee.....eeeeeeee..hhhhh.eeeeee.....eeeeeee......eee.hhhh..eeeeeehhh.eeeeee...hhhhheeeeeeee............eeeee...eeeee........eeeee..hhh.ee..eeeeeeeeeee.....eeee.hhh....eee...ee.....eeeeeeeeee.hhh.....eeeeeehhhheeeeee..... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                4gxv H    1 xVQLVQSGGGVVQPRRSLRLSCAASGFTFSSYAMHWVRQAPGKGLEWVAVISYDGRNKYYADSVKGRFTVSRDNSKNTLYLQMNSLRAEDTSVYYCARELLMDYYDHIGYSPGPTWGQGTLVTVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKRVEPKS  215
                            |       10        20        30        40        50  |     59        69        79   |||  86        96    ||100F|||    107       117       127       137       147       157       167       177       187       197       207        
                            |                                                 52A                            82A||               100A||||||||                                                                                                                   
                            1-PCA                                                                             82B|                100B|||||||                                                                                                                   
                                                                                                               82C                 100C||||||                                                                                                                   
                                                                                                                                    100D|||||                                                                                                                   
                                                                                                                                     100E||||                                                                                                                   
                                                                                                                                      100F|||                                                                                                                   
                                                                                                                                       100G||                                                                                                                   
                                                                                                                                        100H|                                                                                                                   
                                                                                                                                         100I                                                                                                                   


Chain I from PDB  Type:PROTEIN  Length:228
                                                                                                                                                                                                                                                                     
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..eeeee..eee.....eeeeeeee..hhhhh.eeeeee.....eeeeeee......eee.......eeeeeehhh.eeeeee...hhhhheeeeeeee............eeeee...eeeee........eeeee......ee..eeeeeeeeeee.....eeee.hhh....eee...ee.....eeeeeeeeee.........eeeeeehhhheeeeee..... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                4gxv I    1 xVQLVQSGGGVVQPRRSLRLSCAASGFTFSSYAMHWVRQAPGKGLEWVAVISYDGRNKYYADSVKGRFTVSRDNSKNTLYLQMNSLRAEDTSVYYCARELLMDYYDHIGYSPGPTWGQGTLVTVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKRVEPKS  215
                            |       10        20        30        40        50  |     59        69        79   |||  86        96    ||100F|||    107       117       127       137       147       157       167       177       187       197       207        
                            1-PCA                                             52A                            82A||               100A||||||||                                                                                                                   
                                                                                                              82B|                100B|||||||                                                                                                                   
                                                                                                               82C                 100C||||||                                                                                                                   
                                                                                                                                    100D|||||                                                                                                                   
                                                                                                                                     100E||||                                                                                                                   
                                                                                                                                      100F|||                                                                                                                   
                                                                                                                                       100G||                                                                                                                   
                                                                                                                                        100H|                                                                                                                   
                                                                                                                                         100I                                                                                                                   


Chain L from PDB  Type:PROTEIN  Length:214
                                                                                                                                                                                                                                                       
               SCOP domains d4gxvl1 L:1-107 automated matches                                                                               d4gxvl2 L:108-209 automated matches                                                                    SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........eeee.....eeeeee..........eeeeee......eeee.............eeeeee..eeeeee...hhhhheeeeeeeee.....eeee...eeeee........eeeee..hhhhhhh..eeeeeeeeee.....eeeeee..eee...eee...ee.....eeeeeeeeehhhhhhhh..eeeeeee..eeeeeee... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                4gxv L    1 xPVLTQPPSASGSPGQRVTISCSGSSSNIGSYTVNWYQQLPGTAPKLLIYSLNQRPSGVPDRFSGSKSGTSASLAISGLQSEDEAVYYCAAWDDSLSAHVVFGGGTKLTVLGQPKAAPSVTLFPPSSEELQANKATLVCLISDFYPGAVTVAWKADSSPVKAGVETTTPSKQSNNKYAASSYLSLTPEQWKSHRSYSCQVTHEGSTVEKTVAPT  209
                            |       11        21      ||29        39        49        59        69        79        89      ||96       106|      115       125       135       145       155       165       175       185       195       205    
                            1-PCA   9|              27A|                                                                  95A||        106A                                                                                                       
                                    11               27B                                                                   95B|                                                                                                                   
                                                                                                                            95C                                                                                                                   


Chain M from PDB  Type:PROTEIN  Length:214
                                                                                                                                                                                                                                                       
               SCOP domains d4gxvm1 M:1-107 automated matches                                                                               d4gxvm2 M:108-209 automated matches                                                                    SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........eeee.....eeeeee..........eeeeee......eeee.............eeeeee..eeeeee...hhhhheeeeeeeee.....eeee...eeeee........eeeee..hhhhhhh..eeeeeeeeee.....eeeeee..eee...eee...ee.....eeeeeeeeehhhhhhhh..eeeeeee..eeeeeee... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                4gxv M    1 xPVLTQPPSASGSPGQRVTISCSGSSSNIGSYTVNWYQQLPGTAPKLLIYSLNQRPSGVPDRFSGSKSGTSASLAISGLQSEDEAVYYCAAWDDSLSAHVVFGGGTKLTVLGQPKAAPSVTLFPPSSEELQANKATLVCLISDFYPGAVTVAWKADSSPVKAGVETTTPSKQSNNKYAASSYLSLTPEQWKSHRSYSCQVTHEGSTVEKTVAPT  209
                            |       11        21      ||29        39        49        59        69        79        89      ||96       106|      115       125       135       145       155       165       175       185       195       205    
                            1-PCA   9|              27A|                                                                  95A||        106A                                                                                                       
                                    11               27B                                                                   95B|                                                                                                                   
                                                                                                                            95C
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
    → Modified Residue (blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
  x → Chemical Group (purple background, 'x', labelled with number + name, e.g. ACE or NH2)
  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (2, 4)

Asymmetric Unit
(-)
Class: All beta proteins (24004)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4GXV)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4GXV)

(-) Gene Ontology  (0, 0)

Asymmetric Unit(hide GO term definitions)
    (no "Gene Ontology" information available for 4GXV)

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  Cis Peptide Bonds
    Glu H:148 - Pro H:149   [ RasMol ]  
    Glu I:148 - Pro I:149   [ RasMol ]  
    Phe H:146 - Pro H:147   [ RasMol ]  
    Phe I:146 - Pro I:147   [ RasMol ]  
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  4gxv
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 Related Entries

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(-) Related Entries Specified in the PDB File

4gxu 4gxx